A man kills several of his business partners and his estranged ex-wife, then runs away with his children: a young Victoria and baby Lilly. After speeding on a remote, snowy road, he crashes into the woods and takes the children to an abandoned cabin he wanders upon nearby. Realizing the mistakes he has made, he prepares to commit murder suicide but at the last moment is killed by a strange figure in the cabin. Victoria looks at the figure but only sees a blur as her glasses were broken in the crash.

Five years later, their Uncle Lucas (Nikolaj Coster-Waldau) and his girlfriend Annabel (Jessica Chastain) have been madly searching for his brother and nieces using the inheritance of his brother. The searchers stumble upon the crashed car and find the two children in the cabin. In this time, they have become completely like animals, with Victoria physically shielding Lilly in a defensive stance to the intruders. They are put under the care of a psychiatrist, Dr. Dreyfuss. There is a legal dispute over custody of the children between Lucas and a rich aunt on the childrens’ mother’s side, while the court questions the ability of Lucas and Annabel to raise the children in a small apartment with little income given their special needs. Dr. Dreyfuss agrees to recommend Lucas and Annabel as the childrens’ legal guardians as long as they agree to move into a special home used to perform case studies, knowing that he would not be able to monitor their progress if their aunt, who lives on the other side of the country, were to obtain custody.

It quickly becomes apparent that the strange figure, who the children repeatedly refer to as “Mama”, is in the new home with the children. Her history is given throughout the movie through a combination of dreams Anabelle has (induced by Mama), research by Dr. Dreyfuss, and conversations with Victoria. “Mama” was a former patient at a mental asylum in the 1800’s; her appearance and simple actions imply she had Down Syndrome, though this is never officially stated. She breaks out of the asylum and stabs a nun who had taken Mama’s baby (also named Lily) into her care then steals the baby back. Chased by the authorities, she ends up at the edge of a cliff overlooking the lake; seeing no other path, she jumps and hits a tree branch on the way down. While Mama fell into the lake, the baby (killed by the impact) was stuck to the tree trunk and was recovered by the pursuers. Mama becomes a ghost, twisted by the sad emotions of not knowing where her child is (she is unaware of why the baby was not in the lake with her). This causes her to take a form of physically being twisted, with body parts askew and many joints bending the wrong way. She searched the woods for centuries trying to find her baby, until she stumbled upon Victoria and Lily about to be killed in the cabin, and began taking care of the children as her own.

Mama’s presence is generally signaled by black butterflies and electrical problems. She plays with the children but hides from sight of anyone else; Victoria always takes off her glasses when she looks at Mama and tells Dr. Dreyfuss she won’t come where she can be seen. Early in the movie, Lucas is pushed down the stairs by Mama and ends up in a coma. This forces Annabel, who does not want the children, to take care of them. Over time, Victoria becomes more like a normal child, but Lilly retains her animalistic nature; this is attributed to the fact that Victoria was older and thus had socially developed before their abandonment in the woods. Over time, Annabel becomes attached to the children, and later, Victoria begins to prefer her over Mama, but Lilly still remains completely loyal to Mama. Annabel becomes aware there is something wrong and that Mama may indeed be real. Victoria worries for her safety, saying Mama gets very jealous.

Dr. Dreyfuss begins to believe the stories of Mama, first because Victoria is able to tell stories with information she shouldn’t be able to know, and later because he actually sees Mama. In the course of the investigation, he obtains custody of the corpse of Mama’s baby. Dr. Dreyfuss comes to believe that Mama is located in the cabin in the woods and goes to investigate but is killed by Mama there. The aunt believes Annabel is abusing the children (due to bruises Lilly has from her animalistic tendencies) and begins to spy on the house for proof. Lucas has a dream induced by his dead brother while in a coma, asking him to save his children and pointing him to a location in the woods. Annabel visits Dr. Dreyfuss’s office after another supernatural night at the house but finds out he is missing; she steals his objects related to the case. At this point, she learns of the aspects of the case which the doctor had found out about and finds the baby’s corpse. At the same time, Mama becomes angry and attacks the children and Annabel; Victoria tries hard to defend Annabel and pleads for Mama to stop, but Lilly is still clearly loyal to Mama. Annabel is knocked out, but at the last moment the aunt breaks into the house and has her body possessed by Mama. Mama uses this body to take the children to the cabin.

Annabel wakes up, grabs the baby’s corpse, and drives to the lake, finding Lucas along the way, who has left the hospital and gone to the site his brother told him about in his coma dream. They arrive at the cabin, finding the aunt’s corpse but neither Lilly nor Victoria. Annabel sees the cliff that Mama had originally jumped from; remembering the warning that ghosts are twisted souls doomed to repeat their mistakes, she realizes Mama’s intentions to jump off the cliff with the children. Lucas and Annabel arrive in time to stop the children from jumping, but Mama attacks them. The assault is stopped when Mama finds her baby’s corpse, begins crying, and prepares to jump off the cliff with it, her twisted appearance reverting to a more human one. However, as they are leaving, Lilly shouts to Mama and she regains her twisted appearance and attacks again, knocking out Lucas. She grabs the kids and walks to the edge of the cliff. Annabel tries desparately to stop Mama, eventually beaten to the point that she can only hold onto Victoria. Once at the edge of the cliff, Victoria tries to convince Lilly not to go, and Lilly cries that Lilly, Victoria, and Mama should all be together. Mama jumps off the cliff with just Lilly, and upon hitting the branch, Mama and Lilly turn into a shower of butterflies. The movie ends with Victoria realizing that one of the butterflies watching over her is in fact Lilly, perhaps referencing a ghostly regret of Victoria not going with her.

Alcoholic Freddie Quell (Joaquin Phoenix) is a World War II veteran suffering from post-traumatic stress disorder and struggling to adjust to a post-war society. He finds a job as a photographer at a local department store taking family portraits, but is eventually fired for assaulting a customer after drunkenly harassing him. Freddie then finds work on a cabbage farm, but one of his home-made alcoholic beverages poisons an elderly coworker due to its questionable contents. Freddie is chased off the farm by his employers and becomes a drifter.

One night, Freddie, while intoxicated, boards the yacht of Lancaster Dodd (Philip Seymour Hoffman), the leader of a philosophical movement known as The Cause. Despite Freddie’s intrusion, Dodd allows Freddie to stay because he enjoys his drinks (revealed to be made with paint thinner), even going so far as to extend an invitation to Freddie to attend the marriage of Dodd’s daughter (Ambyr Childers). Dodd exposes Freddie to the exercise known as Processing, during which Freddie is subjected to heavy psychological questioning with the intent of conquering any past traumas Freddie may have. It is revealed that his father has died, his mother is institutionalized, he may have had an incestuous relationship with his aunt, and he abandoned the love of his life, a young girl named Doris (Madisen Beaty) who wrote to him while he was at war. Freddie takes a liking to The Cause, and Dodd sees something exceptional in Freddie. Together they begin to travel along the East Coast spreading the teachings of The Cause. However, Freddie’s violent and erratic behavior has not improved, nor has his alcoholism. At a dinner party in New York, a man questions Dodd’s methods and statements, and Freddie responds by assaulting him later in the night.

Other members of The Cause begin to worry about Freddie’s behavior, despite Dodd’s insisting that Freddie is an important part of the movement. While visiting in Philadelphia, Dodd’s wife Peggy (Amy Adams) tells Freddie that he must quit drinking if he wishes to stay, to which he agrees. However, he has no true intention of keeping his promise. Freddie criticizes Dodd’s son Val (Jesse Plemons) for disregarding his father’s teachings, but he responds by informing Freddie that his father is a fraud and all of his teachings are being improvised. Dodd is arrested for practicing medicine without proper qualifications, and Freddie is also arrested for assaulting police officers. When he is imprisoned, he responds by destroying parts of his jail cell and smashing his head on the top bunk bed. Dodd attempts to calm him down from the neighboring cell but Freddie erupts in a tirade, questions everything that Dodd has taught him and accuses him of being a fake. The two men trade insults until Dodd turns his back. They eventually reconcile upon their release, but members of The Cause have become more suspicious and fearful of Freddie, believing him to be insane or an undercover agent.

Freddie returns to the exercises performed by The Cause, but becomes increasingly angry and frustrated with his lack of results and repetition of the exercises. Eventually he passes the tests, with Dodd hugging him in approval. They travel to Phoenix, Arizona to release Dodd’s latest work, which he was initially hesitant to publish. When Dodd’s publisher criticizes the quality of the book and its teachings to Freddie, Freddie drags him outside and assaults him. Helen Sullivan (Laura Dern), a key member of The Cause, upon reading the book, questions Dodd for contradicting previously-established practices in the new book, and Dodd loses his temper publicly. During another exercise in which Freddie is supposed to ride a motorcycle at high speed through the desert towards an object in the distance, he instead abandons Dodd, rides the motorcycle out of the desert, and decides to leave The Cause. He attempts to rekindle his relationship with Doris, but learns from her mother that seven years have passed since he last saw her and that she is now happily married with children and is living in Alabama. Freddie leaves disappointed, but seems pleased that Doris has made a happy life for herself.

While sleeping in a movie theater, Freddie has a “vision” of Dodd, who calls him by telephone, having mysteriously located him. Dodd informs Freddie that he is now residing in England and that Freddie must travel and join him as soon as possible. Taking the dream literally, he travels across the Atlantic to reunite with Dodd. Upon Freddie’s arrival at Dodd’s school, Peggy concludes that Freddie has no intention of improving his life and should not be involved in The Cause at all. Dodd finally realizes that his wife is correct, and that Freddie must venture out to the world and take his own path. He gives Freddie an ultimatum: Stay with The Cause and devote himself to it for the rest of his life, or leave and never come back. Freddie decides to leave. After leaving, he meets a woman at a pub and has sex with her, while reciting the questions Dodd had first posed to him during their first session at sea. The film ends with the image of Freddie on the beach, lying in the sand, next to the sand sculpture of a woman he had earlier defiled.